ASI Masterclass - Workshop
Thomas Ashhurst, Givanna Putri, Felix Marsh-Wakefield, Jennifer Habel, Wuji Zhang
26/10/2021
As part of the Australia and New Zealand Society for Immunology (ASI) IgV Masterclass (25-26 October 2021), we will be running an online hands-on workshop on high-dimensional analysis approaches to investigate the immune response to COVID-19 in the blood and respiratory tract.
You can join the workshop via this link:
Workshop schedule (Tue 26-Oct)
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Introduction Tue 26-Oct, 10:00 am - 10:30 am AEDT The workshop day (Tue 26-Oct) will start off with some opening remarks on COVID-19 and respiratory immunology from Thomas Ashhurst, Oanh Nguyen, and Katherine Kedzierska.
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Session #1: Getting started with cytometry analysis using Spectre and R Tue 26-Oct, 10:30 am – 12:00 pm AEDT Lead instructors: Givanna Putri, Felix Marsh-Wakefield In this session, instructors will introduce attendees to methods of high-dimensional analysis with R/RStudio. Specifically we will use the R package Spectre, and will explore computational approaches such as clustering (e.g. using FlowSOM) and dimensionality reduction (e.g. using tSNE or UMAP).
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Session #2: High-dimensional analysis of immune responses to COVID-19 in perhiperhal blood Tue 26-Oct, 1:00 pm – 2:30 pm AEDT Lead instructors: Felix Marsh-Wakefield, Jennifer Habel In this session we will be investigating the immune response to COVID-19 in perihperal blood. We will compare immune responses in healthy controls, convalescent patients, and patients with mild COVID-19 or severe COVID-19.
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Session #3: High-dimensional analysis of immune responses to COVID-19 in the respiratory tract Tue 26-Oct, 3:00 pm – 4:30 pm Lead instructors: Givanna Putri, Wuji Zhang In this session we will be investigating the immune response to COVID-19 in the respiratory tract, from samples acquired via an endotracheal tube. In particular we will explore a variety of myeloid cells that infiltrate the respiratory tract via the blood, including macrophages and neutrophils, and how they compare to similar cells in the blood.
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Preparation
Analysis using R/RStudio
In this workshop we will be using R & RStudio to analyse cells from the blood or respiratory tract of COVID-19 patients, measured by flow cytometry. We will be using the R package ‘Spectre’ to do this. The instructors will guide attendees through the analysis process in R, stopping regularly to discuss what has been done, and what we can observe about the COVID-19 immune response.
Following along at home
You are welcome to simply watch, take notes, and ask questions. If you would like to replicate the analysis process yourself, following the instructors, then we have provided access to the datasets and R scripts that we will use. You can either do this on your own laptop, or you can use one of the ‘virtual’ computers that we provide access to, with the software and datasets pre-installed.
Download links should have been emailed to you. If you did not receive the links, please email thomas.ashhurst@sydney.edu.au.
Option 1: just watch and ask questions
- No need to do anything, just join the zoom session and ask questions!
Option 2: follow along on a virtual computer
- Follow these instructions to access the virtual computers (with datasets, software, and scripts pre-installed)
- You will find the workshop much easier if you check out these introductory tutorials to R/Rstudio and Spectre ahead of time
- During the sessions, join the zoom session and follow along with us
Option 3: follow along on your own computer
- Firstly, you will need to download R and RStudio
- Once you have done that, you will need to install the Specte R package
- Finally, you will find the workshop much easier if you check out these introductory tutorials to R/Rstudio and Spectre ahead of time
- During the sessions, join the zoom session and follow along with us
Datasets
The COVID-19 datasets used in this workshop originate from these two studies from the Kedzierska Laboratory: Koutsakos et al 2021 and Zhang et al 2021. To prepare them for this workshop we have performed some initial cleanup and batch alignment. We will discuss the exact preparation steps during the workshop.
Feel free to use these datasets during and after the workshop,but we would request that you don’t share these widely with others, or post them on a publically accessible platform.
INTRODUCTION (10:00 am)
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Introduction Tue 26-Oct, 10:00 am - 10:30 am AEDT The workshop day (Tue 26-Oct) will start off with some opening remarks on COVID-19 and respiratory immunology from Thomas Ashhurst, Oanh Nguyen, and Katherine Kedzierska.
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SESSION 1 - Intro to R (10:30 am)
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Session #1: Getting started with cytometry analysis using Spectre and R Tue 26-Oct, 10:30 am – 12:00 pm AEDT Lead instructors: Givanna Putri, Felix Marsh-Wakefield In this session, instructors will introduce attendees to methods of high-dimensional analysis with R/RStudio. Specifically we will use the R package Spectre, and will explore computational approaches such as clustering (e.g. using FlowSOM) and dimensionality reduction (e.g. using tSNE or UMAP).
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Open R script
To get started, find the relevant R script and open it in RStudio.
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#### Coming soon
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SESSION 2 - blood (1:00 pm)
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Session #2: High-dimensional analysis of immune responses to COVID-19 in perhiperhal blood Tue 26-Oct, 1:00 pm – 2:30 pm AEDT Lead instructors: Felix Marsh-Wakefield, Jennifer Habel In this session we will be investigating the immune response to COVID-19 in perihperal blood. We will compare immune responses in healthy controls, convalescent patients, and patients with mild COVID-19 or severe COVID-19.
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Open R script
To get started, find the relevant R script and open it in RStudio.
#######################################################################################################
#### Coming soon
#######################################################################################################
SESSION 3 - respiratory (3:00 pm)
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Session #3: High-dimensional analysis of immune responses to COVID-19 in the respiratory tract Tue 26-Oct, 3:00 pm – 4:30 pm Lead instructors: Givanna Putri, Wuji Zhang In this session we will be investigating the immune response to COVID-19 in the respiratory tract, from samples acquired via an endotracheal tube. In particular we will explore a variety of myeloid cells that infiltrate the respiratory tract via the blood, including macrophages and neutrophils, and how they compare to similar cells in the blood.
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Script
#######################################################################################################
#### Coming soon
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